Align D-xylose transporter; D-xylose-proton symporter (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter
Query= SwissProt::O52733 (457 letters) >FitnessBrowser__Koxy:BWI76_RS03110 Length = 499 Score = 307 bits (787), Expect = 4e-88 Identities = 180/449 (40%), Positives = 276/449 (61%), Gaps = 13/449 (2%) Query: 9 VYFFGALGGLLFGYDTGVISGAILFIQKQMNLGSWQQGWVVSAVLLGAILGAAIIGPSSD 68 V LGGLLFGYDTGVISGA+LF+ +++L + G V S++L GA GA + G ++ Sbjct: 28 VALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVTSSLLFGAAFGALLSGNLAN 87 Query: 69 RFGRRKLLLLSAIIFFVGALGSAFSPEFWTLIISRIILGMAVGAASALIPTYLAELAPSD 128 GR+K++L A++F +GA+G++ +P+ +I R+ILG+AVG A+A +P Y+AE+AP++ Sbjct: 88 AAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVAVGGAAATVPVYIAEIAPAN 147 Query: 129 KRGTVSSLFQLMVMTGILLAYITNYSFSGFYTG---WRWMLGFAAIPAALLFLGGLILPE 185 KRG + +L +LM+++G LLAYI+N +F + G WRWML A +PA LL+ G + +P+ Sbjct: 148 KRGQLVTLQELMIVSGQLLAYISNATFHEVWGGESTWRWMLAVATLPAVLLWFGMMFMPD 207 Query: 186 SPRFLVKSGHLDEARHVLD-TMNKHDQVAVNKEIND-IQESAKIVSGGWSELFGKMVRPS 243 SPR+ G L EAR VL+ T +K D EI + + E + +SE+ + Sbjct: 208 SPRWYAMKGRLAEARRVLERTRHKDDVEWELLEITETLDEQRNLGKPRFSEIMTPWLFKL 267 Query: 244 LIIGIGLAIFQQVMGCNTVLYYAPTIFTDVGFGVSAALLAHIGIGIFNVIVTAIAVAIMD 303 +IGIG+A+ QQ+ G NT++YYAPT+ T VG +AAL A I G+ +V++T + + ++ Sbjct: 268 FMIGIGIAVIQQLTGVNTIMYYAPTVLTSVGMTDNAALFATIANGVVSVLMTFVGIWMLG 327 Query: 304 KIDRKKIVNIGAVGMGISL-FVMSIGM---KFSGGSQTA--AIISVIALTVYIAFFSATW 357 KI R+ + IG G L F+ ++ + G A A + + + ++++F Sbjct: 328 KIGRRPMTMIGQFGCTACLVFIGAVSYLLPETVNGQPDALRAYMVLAGMLLFLSFQQGAL 387 Query: 358 GPVMWVMIGEVFPLNIRGLGNSFASVINWTANMIVSLTFPSLLDFFG-TGSLFIGYGILC 416 PV W+++ E+FP +RG+ A W AN ++SL FP LL + G +G+ FI GI Sbjct: 388 SPVTWLLMSEIFPTRLRGIFMGGAVFSMWIANFLISLFFPILLAWLGLSGTFFIFAGIGV 447 Query: 417 FASIWFVQKKVFETRNRSLEDIEATLRAK 445 F +I FV K V ETR+RSLE IE LR K Sbjct: 448 FGAI-FVIKCVPETRHRSLEQIEHYLRDK 475 Lambda K H 0.327 0.141 0.424 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 622 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 457 Length of database: 499 Length adjustment: 34 Effective length of query: 423 Effective length of database: 465 Effective search space: 196695 Effective search space used: 196695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory